Gromacs

specbond.dat

    Table of contents
    1. 1. Contents

    The specbond.dat file contains information pdb2gmx requires in order to generate correct topologies for structures with unusual bonds, such as disulfides, or heme links. You may need to edit such a file in order to add your own special bond of interest. In such a case, copy the original file from the GROMACS installation directory to your working directory and edit the local copy.

     

    Contents

    The default contents of specbond.dat (version 4.5) is as follows:

    8
    CYS     SG      1       CYS     SG      1       0.2     CYS2    CYS2
    CYS     SG      1       HEM     FE      2       0.25    CYS2    HEME
    CYS     SG      1       HEM     CAB     1       0.18    CYS2    HEME
    CYS     SG      1       HEM     CAC     1       0.18    CYS2    HEME
    HIS     NE2     1       HEM     FE      1       0.2     HIS1    HEME
    MET     SD      1       HEM     FE      1       0.24    MET     HEME
    CO      C       1       HEME    FE      1       0.19    CO      HEME
    CYM     SG      1       CYM     SG      1       0.2     CYS2    CYS2
    
     

    The nine columns respectively indicate

    1. residue name A
    2. atom name A
    3. number of bonds that this atom can form
    4. residue name B
    5. atom name B
    6. number of bonds that this atom can form
    7. the reference length for searching for candidate bonds, the margin is ±10%
    8. the new name for residue A
    9. the new name for residue B

    To describe new possible special bonds, such as disulfides, so that pdb2gmx can generate them for you, you should add new lines similar to these example lines, and update the counter in the first line.

    To generate such a bond, you then need to present a structure to pdb2gmx with the residues and atoms named as above, and the two atoms forming the bond within the cutoff listed above. To make this work you have to put all the branches in one [ moleculetype ] with pdb2gmx -merge (in GROMACS 4.0) or some suitable use of pdb2gmx -chainsep (in GROMACS 4.5 and later).

     

    This procedure can also be used to generate branched or circular polymers.

    Page last modified 11:33, 11 Jan 2012 by mabraham